A comparative evaluation of genome assembly reconciliation tools

Genome Biology
Hind AlhakamiStefano Lonardi

Abstract

The majority of eukaryotic genomes are unfinished due to the algorithmic challenges of assembling them. A variety of assembly and scaffolding tools are available, but it is not always obvious which tool or parameters to use for a specific genome size and complexity. It is, therefore, common practice to produce multiple assemblies using different assemblers and parameters, then select the best one for public release. A more compelling approach would allow one to merge multiple assemblies with the intent of producing a higher quality consensus assembly, which is the objective of assembly reconciliation. Several assembly reconciliation tools have been proposed in the literature, but their strengths and weaknesses have never been compared on a common dataset. We fill this need with this work, in which we report on an extensive comparative evaluation of several tools. Specifically, we evaluate contiguity, correctness, coverage, and the duplication ratio of the merged assembly compared to the individual assemblies provided as input. None of the tools we tested consistently improved the quality of the input GAGE and synthetic assemblies. Our experiments show an increase in contiguity in the consensus assembly when the original assembl...Continue Reading

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Citations

Mar 29, 2019·Bioinformatics·Pierre MarijonJean-Stéphane Varré
Jun 29, 2018·Bioinformatics·Weihua PanStefano Lonardi
May 26, 2020·BMC Bioinformatics·Michael Gruenstaeudl, Nils Jenke
Aug 8, 2020·Bioinformatics·Luyu Xie, Limsoon Wong
Nov 13, 2020·PLoS Computational Biology·Hyungtaek JungSeong-Il Eyun
Jan 2, 2021·Frontiers in Genetics·Soma S MarlaRajesh Kumar
May 20, 2021·Cell Reports·Peter A LarsonMariano Sanchez-Lockhart
Jun 30, 2021·Algorithms for Molecular Biology : AMB·Sven SchrinnerGunnar W Klau
Jul 31, 2021·Briefings in Bioinformatics·Amarinder Singh ThindBruce Ashford
Nov 10, 2021·G3 : Genes - Genomes - Genetics·Kameron T WittmeyerKeith R Hopper

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Methods Mentioned

BETA
CISA
SGA

Software Mentioned

Linux Ubuntu
MSR
MIX ZORRO
MAIA
CA
LG
IDBA
NGS
SPAdes
eRGA

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